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<title>PyTom: Tutorial</title>
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<p class="Header">
	PyTom: Files
</p>
<h2 id="General">Big data</h2>
<p class="textBody">
Big data such as raw projections from the microscope, tomograms and subtomograms is stored in binary on disk. PyTom currently supports three filetypes:
  <ul>
	  <li>
	    <p>EM files (<a href="emFileType.html">specification</a>)</p>
	  </li>
	  <li>
	    <p>MRC Files (<a href="http://ami.scripps.edu/software/mrctools/mrc_specification.php">specification</a>)</p>
	  </li>
	  <li>
	    <p>CCP4 Files (<a href="http://www.ccp4.ac.uk/html/maplib.html#description">specification</a>)</p>
	  </li>
  </ul>     
In general, all files stored in these filetypes can be read into memory by the <code>pytom.basic.files.read</code> function if you write your own code or use PyTom in the terminal. 
If you however want to convert filetypes from <strong>EM</strong> to say <strong>MRC</strong>, you can use the conversion scipts in <code>pytom/bin</code> like
<code>em2mrc.py</code>, <code>em2ccp4.py</code> to do this job. We provide all combinations.
 
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<h2 id="General">PDB to electron density conversion</h2>
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You can use our <code>pdb2em.py</code> script to convert PDB files to electron densities.

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		<code>
			<pre>
NAME
    pdb2em.py
DESCRIPTION
    Compile a electron density from PDB file
                          http://pytom.org/doc/pytom/files.html
OPTIONS
    -p, --pdbFile    A PDB file (Is optional: No; Requires arguments: Yes)
    -c, --chain    A Chain (Is optional: Yes; Requires arguments: Yes)
    -s, --pixelSize    Pixel size of output volume (Is optional: Yes; Requires arguments: Yes)
    -v, --volumeSize    Volume length (size) in all dimensions (Is optional: Yes; Requires arguments: Yes)
    -o, --outputVolumePath    Path to output volume  (Is optional: No; Requires arguments: Yes)
    -h, --help    Help. (Is optional: Yes; Requires arguments: No)
			</pre>
		</code>
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</p>
<h2 id="General">XML Files</h2>
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	We use PyTom XML files to store metadata of binaries files like projections and tomograms. Furthermore, XML is a good tool to store information about processing jobs as well.
	Hence, XML files are used like a databank which remains open and, more importantly, readable to the user all time. It can be adjusted to the current requirements of the project 
	using a standard text editor.  
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